MACS or Homer. Homer has a few peak calling modes that control the type and size of peaks it finds. MACS is more of a straight ahead peak caller that just looks for peaks of any width. at least that's how I think of the two.

Hi all,
And what about MeDIP-seq (not ChIP-seq)? I guess the answer would be the same, but what parameters keep/change?
I'm working on a Illumina IP library (50 bp SE) made after inmunoprecipitate genomic DNA fragments with antibodies which detect methylated bases. I've seen one paper using MACS with these kind of data, thought no specify any parameters used. Right now, I don't have control/input.
Eg. after using MACS, it says no paired peaks were found so I should go with the --nomodel option, but I'm guessing about --shiftsize since there is no TF I'm looking for (just nucleotide methylation); would it be important that --shiftsize number?
One more thing I'd like to ask is, not having control/input I've heard I should use the --nolambda option. Actually that's from this ppt tutorial:http://www.slideshare.net/lucacozzuto/macs-course

I am trying to analyze data for factor which does not behave typically as transcription factor. I used macs and homer for peak calling. macs2 is giving me hardly 20-30 peaks while Homer is giving about 20000 peaks. macs2 is not picking up peaks which i can easily visualize in IGV. How can i be sure which peak caller to use and how can I filter peaks from Homer data (based on what criteria)